Supplementary Figure 4: Whole-blood transcriptional analyses suggest macrophage activation and compensatory upregulation of apoptosis and hematopoiesis distinct from NOMID.
Whole-blood RNA sequencing was performed (Online Methods). Functional gene lists were generated (Supplementary Table 2), and genes showing differential regulation in the NLRC4-MAS patient’s flare sample versus samples from healthy controls and NOMID patients were selected. The other samples included were drawn from the NLRC4-MAS patient before the initiation of IL-1 receptor antagonist treatment with inactive disease (pre), after IL-1Ra treatment (post) or from matched samples from seven NOMID patients with active disease before the initiation of IL-1Ra treatment (NOMID pre) or with inactive disease after the initiation of IL-1Ra treatment (NOMID post). Transcript levels were normalized to the average expression of the same transcript in five healthy pediatric controls (HC) and are expressed as the fold change (FC). Transcripts that are upregulated (UP) or downregulated (DN) in the flare sample are separated for NOMID patients for clarity. (a) Downregulation of NLRP1, NLRP3 and associated genes (MEFV, HSP90AB1 and SUGT1) and of NOD2 was seen in NLRC4-MAS but not in NOMID, whereas upregulation of NLRC4, AIM2 and NLRP6 was seen in both conditions. (b) Downregulation of various lymphocyte (CCL3, CCR3, CCR4 and CCR7) and neutrophil (IL8 and CXCR2) chemokines and chemokine receptors (with the exception of CXCR2) was observed in NLRC4-MAS but not in NOMID. (c) Upregulation of apoptotic factors (BCL2A1, BIK, BAD and LTB4R) and downregulation of antiapoptotic factors (TP53, BCL2 and CD40LG) were present in NLRC4-MAS but minimal in NOMID. Downregulation of the proapoptotic gene DIABLO was inconsistent with this paradigm and was not observed in NOMID. (d) Downregulation of genes associated with interferon production (STAT4) or signaling (IFNAR2, JAK1, STAT1 and STAT2) was observed in the flare sample. Only JAK3 upregulation was observed in both NLRC4-MAS and active NOMID. (e) Dysregulation of markers of classical (TLR5, IL7R, PTGS2 and HIF1A) and alternative (ARG1, DECTIN1 and IL1R2) macrophage activation. Upregulated genes were similarly regulated in NLRC4-MAS and NOMID.
